Contacts of the helix formed by residues 258 - 264 (chain A) in PDB entry 4WMB
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with PRO 258 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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257A GLN* 1.4 84.3 - - + +
259A VAL* 1.3 62.2 + - - +
260A TYR 3.2 2.9 - - - -
261A ARG* 3.2 8.9 + - + +
262A HIS* 3.1 20.6 + - - +
359A TRP* 4.2 8.5 - - + -
364A TYR* 3.5 38.7 - - + -
367A VAL* 4.8 0.2 - - + -
368A PHE* 3.5 22.4 - - + -
371A TYR* 3.7 44.0 - - + -
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Residues in contact with VAL 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A GLU* 3.4 38.6 - - + +
257A GLN* 3.0 3.5 + - + +
258A PRO* 1.3 76.4 - - - +
260A TYR* 1.3 73.9 + - + +
262A HIS* 3.2 6.3 + - - +
263A THR* 2.9 37.6 + - - +
327A LEU* 4.7 9.4 - - + -
330A GLN* 5.1 0.2 - - - +
359A TRP* 3.5 46.6 - - + +
1B BGC 3.8 7.6 - - - +
2B XYS 4.2 7.6 - - - +
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Residues in contact with TYR 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255A GLU* 4.1 3.1 - - + -
257A GLN 4.6 0.8 + - - -
258A PRO 3.2 0.8 - - - -
259A VAL* 1.3 90.5 - - + +
261A ARG* 1.3 65.7 + - - +
262A HIS 3.1 1.1 - - - -
263A THR* 3.8 15.3 - - + -
264A PHE* 2.9 48.9 + + + +
277A GLY* 4.2 5.1 - - - -
285A PRO 3.3 31.6 + - - +
286A GLY* 3.8 6.3 - - - -
287A PHE 3.5 13.9 - - - -
323A PHE* 4.0 10.8 - + - -
327A LEU* 4.4 1.7 - - + +
330A GLN* 3.2 29.8 + - - +
331A ASP* 2.5 32.1 + - - -
334A THR* 3.3 32.8 - - + -
338A MET* 5.0 0.4 - - + -
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Residues in contact with ARG 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258A PRO* 3.2 14.3 + - + +
260A TYR* 1.3 79.3 - - - +
262A HIS* 1.3 60.4 + - - +
265A TRP* 3.7 10.2 + - - +
268A ARG* 3.2 57.4 - - - +
277A GLY* 3.4 22.3 + - - +
278A ASP* 4.3 1.4 + - - -
279A PRO* 3.7 16.6 - - - +
285A PRO 5.3 0.2 + - - -
364A TYR* 3.6 30.3 - - + -
367A VAL* 3.4 36.5 - - - +
371A TYR* 2.8 25.4 + - + +
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Residues in contact with HIS 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258A PRO 3.1 5.5 + - - +
259A VAL 3.3 8.7 - - - +
260A TYR 3.1 0.4 - - - -
261A ARG* 1.3 76.7 - - - +
263A THR* 1.3 70.0 + - - +
265A TRP* 3.3 21.5 - - - +
359A TRP* 3.5 33.2 - + + -
362A HIS 5.5 0.2 - - - -
364A TYR* 2.7 35.9 + + + +
54D ASN 3.2 11.7 + - - -
55D PRO 3.2 24.5 - - - -
56D CYS 2.9 20.1 + - - -
57D LEU* 3.4 25.6 - - + +
74D PRO* 4.5 2.9 - - + -
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Residues in contact with THR 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259A VAL* 2.9 25.5 + - - +
260A TYR* 3.4 17.6 + - + -
262A HIS* 1.3 79.7 - - - +
264A PHE* 1.3 58.3 + - - +
265A TRP* 3.2 2.7 + - - +
266A GLN 5.1 0.3 + - - -
322A HIS 4.4 11.8 - - - +
323A PHE* 3.8 31.5 - - + -
324A ARG 3.2 27.9 + - - +
325A GLY* 5.2 0.7 - - - -
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Residues in contact with PHE 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260A TYR* 2.9 36.5 + + + +
261A ARG 4.0 0.4 - - - -
263A THR* 1.3 76.7 - - - +
265A TRP* 1.3 58.7 + - - +
266A GLN 3.3 2.5 - - - -
267A PHE* 3.1 8.9 + - + +
268A ARG* 2.8 36.4 + - + +
276A VAL* 3.5 26.2 - - + +
277A GLY* 5.0 0.9 - - - -
321A TYR* 3.7 42.6 - + + -
323A PHE* 3.3 41.1 - + - -
334A THR* 3.9 12.1 - - + -
335A MET* 4.5 4.0 - - - -
338A MET* 3.7 31.9 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il